Sounds like you budgeted money you don't have yet, and you don't have a Buffer either.
No Problem!! At least you got started. To answer your immediate question, I'd just budget what you have now toward those Categories where you will need to make payments before your next check comes in. Budget it all down to zero, and don't worry yet about what will come out of the next check. If you've got all the bills covered, and still have some left, budget that to the next priorities after the next check is due.
Then when that check comes in Categorize it as Available This Month, and revisit your Budget, Budgeting down to zero again, prioritizing toward the expenses you expect to have to meet before the check after that comes in. Keep doing this until the First of April. If you are lucky, you'll have some left over which can be used to start budgeting for April. Eventually, if you NEVER spend more than you budget (and you can move money around in your budget from Category to Category, or even unBudget it and let YNAB carry it over for you to next month), you will build a Buffer and will be living by Rule One, which, like Rome wasn't built in a day (or even a month).
Meantime, follow these links and pick out some free teaching aids:
http://www.youneedabudget.com/support/ynab-coaching/http://www.youneedabudget.com/support/tutorials/Good luck, and come back here often,
Kirk
Mr. Thompson...you're time is up.